.TH g_angle 1 "Thu 26 Aug 2010" "" "GROMACS suite, VERSION 4.5"
.SH NAME
g_angle - calculates distributions and correlations for angles and dihedrals

.B VERSION 4.5
.SH SYNOPSIS
\f3g_angle\fP
.BI "\-f" " traj.xtc "
.BI "\-n" " angle.ndx "
.BI "\-od" " angdist.xvg "
.BI "\-ov" " angaver.xvg "
.BI "\-of" " dihfrac.xvg "
.BI "\-ot" " dihtrans.xvg "
.BI "\-oh" " trhisto.xvg "
.BI "\-oc" " dihcorr.xvg "
.BI "\-or" " traj.trr "
.BI "\-[no]h" ""
.BI "\-[no]version" ""
.BI "\-nice" " int "
.BI "\-b" " time "
.BI "\-e" " time "
.BI "\-dt" " time "
.BI "\-[no]w" ""
.BI "\-xvg" " enum "
.BI "\-type" " enum "
.BI "\-[no]all" ""
.BI "\-binwidth" " real "
.BI "\-[no]periodic" ""
.BI "\-[no]chandler" ""
.BI "\-[no]avercorr" ""
.BI "\-acflen" " int "
.BI "\-[no]normalize" ""
.BI "\-P" " enum "
.BI "\-fitfn" " enum "
.BI "\-ncskip" " int "
.BI "\-beginfit" " real "
.BI "\-endfit" " real "
.SH DESCRIPTION
\&g_angle computes the angle distribution for a number of angles
\&or dihedrals. This way you can check whether your simulation
\&is correct. With option \-ov you can plot the average angle of
\&a group of angles as a function of time. With the \-all option
\&the first graph is the average, the rest are the individual angles.


\&With the \-of option g_angle also calculates the fraction of trans
\&dihedrals (only for dihedrals) as function of time, but this is
\&probably only fun for a selected few.


\&With option \-oc a dihedral correlation function is calculated.


\&It should be noted that the indexfile should contain
\&atom\-triples for angles or atom\-quadruplets for dihedrals.
\&If this is not the case, the program will crash.


\&With option \fB \-or\fR a trajectory file is dumped containing cos and
\&sin of selected dihedral angles which subsequently can be used as
\&input for a PCA analysis using \fB g_covar\fR.
.SH FILES
.BI "\-f" " traj.xtc" 
.B Input
 Trajectory: xtc trr trj gro g96 pdb cpt 

.BI "\-n" " angle.ndx" 
.B Input
 Index file 

.BI "\-od" " angdist.xvg" 
.B Output
 xvgr/xmgr file 

.BI "\-ov" " angaver.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-of" " dihfrac.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-ot" " dihtrans.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oh" " trhisto.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-oc" " dihcorr.xvg" 
.B Output, Opt.
 xvgr/xmgr file 

.BI "\-or" " traj.trr" 
.B Output, Opt.
 Trajectory in portable xdr format 

.SH OTHER OPTIONS
.BI "\-[no]h"  "no    "
 Print help info and quit

.BI "\-[no]version"  "no    "
 Print version info and quit

.BI "\-nice"  " int" " 19" 
 Set the nicelevel

.BI "\-b"  " time" " 0     " 
 First frame (ps) to read from trajectory

.BI "\-e"  " time" " 0     " 
 Last frame (ps) to read from trajectory

.BI "\-dt"  " time" " 0     " 
 Only use frame when t MOD dt = first time (ps)

.BI "\-[no]w"  "no    "
 View output xvg, xpm, eps and pdb files

.BI "\-xvg"  " enum" " xmgrace" 
 xvg plot formatting: \fB xmgrace\fR, \fB xmgr\fR or \fB none\fR

.BI "\-type"  " enum" " angle" 
 Type of angle to analyse: \fB angle\fR, \fB dihedral\fR, \fB improper\fR or \fB ryckaert\-bellemans\fR

.BI "\-[no]all"  "no    "
 Plot all angles separately in the averages file, in the order of appearance in the index file.

.BI "\-binwidth"  " real" " 1     " 
 binwidth (degrees) for calculating the distribution

.BI "\-[no]periodic"  "yes   "
 Print dihedral angles modulo 360 degrees

.BI "\-[no]chandler"  "no    "
 Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi  \-60 || phi  60.

.BI "\-[no]avercorr"  "no    "
 Average the correlation functions for the individual angles/dihedrals

.BI "\-acflen"  " int" " \-1" 
 Length of the ACF, default is half the number of frames

.BI "\-[no]normalize"  "yes   "
 Normalize ACF

.BI "\-P"  " enum" " 0" 
 Order of Legendre polynomial for ACF (0 indicates none): \fB 0\fR, \fB 1\fR, \fB 2\fR or \fB 3\fR

.BI "\-fitfn"  " enum" " none" 
 Fit function: \fB none\fR, \fB exp\fR, \fB aexp\fR, \fB exp_exp\fR, \fB vac\fR, \fB exp5\fR, \fB exp7\fR or \fB exp9\fR

.BI "\-ncskip"  " int" " 0" 
 Skip N points in the output file of correlation functions

.BI "\-beginfit"  " real" " 0     " 
 Time where to begin the exponential fit of the correlation function

.BI "\-endfit"  " real" " \-1    " 
 Time where to end the exponential fit of the correlation function, \-1 is until the end

.SH KNOWN PROBLEMS
\- Counting transitions only works for dihedrals with multiplicity 3

.SH SEE ALSO
.BR gromacs(7)

More information about \fBGROMACS\fR is available at <\fIhttp://www.gromacs.org/\fR>.
